In this study, the 17,694-bp long complete mitochondrial genome (mitogenome) of the dwarf honeybee, Apis florea (Hymenoptera: Apidae), was described, and a noteworthy triplicated tRNA(ser)(AGN) region and an extraordinary long A+T-rich region with repeat regions were identified. The gene arrangement of A. florea mitogenome was identical to that of Apis mellifera, but it contained three tRNA(Ser)(AGN), each of which was preceded by a 44-bp-long repeat unit and followed by a 64-bp-long repeat unit plus one complete first repeat adjacent to tRNA(Met). A total of 1610-bp long two repeat regions in 1987-bp long A+T-rich region were composed of nearly identical 141-219-bp long 5 tandem repeats and 50-52-bp long 12 tandem repeats that were encompassed by three non-repeat sequences. One potential explanation for this repeat sequence is slipped-strand mispairing and unequal crossing-over events during DNA replication.